datamodel/compbio/data/sequence/FastaReader.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0\r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 package compbio.data.sequence;\r
  19 \r
  20 import java.io.File;\r
  21 import java.io.FileNotFoundException;\r
  22 import java.io.InputStream;\r
  23 import java.util.Iterator;\r
  24 import java.util.Scanner;\r
  25 import java.util.regex.MatchResult;\r
  26 \r
  27 import compbio.util.Util;\r
  28 \r
  29 /**\r
  30  * Reads files with FASTA formatted sequences. All the information in the FASTA\r
  31  * header is preserved including trailing white spaces. All the white spaces are\r
  32  * removed from the sequence.\r
  33  * \r
  34  * Examples of the correct input:\r
  35  * \r
  36  * <pre>\r
  37  * \r
  38  * >zedpshvyzg\r
  39  * GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD\r
  40  * \r
  41  * >xovkactesa\r
  42  * CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM\r
  43  * FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG\r
  44  * FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH\r
  45  * DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC\r
  46  * \r
  47  * >ntazzewyvv\r
  48  * CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD\r
  49  * EASINM       AQQWRSLPPSRIMKLNG       HGCDCMHSHMEAD   DTKQSGIKGTFWNG  HDAQWLCRWG      \r
  50  * EFITEA       WWGRWGAITFFHAH  ENKNEIQECSDQNLKE        SRTTCEIID   TCHLFTRHLDGW \r
  51  *   RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN    \r
  52  *   W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF   \r
  53  *   FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI\r
  54  * \r
  55  *    > 12 d t y wi             k       jbke    \r
  56  *   KLSHHDCD\r
  57  *    N\r
  58  *     H\r
  59  *     HSKCTEPHCGNSHQMLHRDP\r
  60  *     CCDQCQSWEAENWCASMRKAILF\r
  61  * \r
  62  * </pre>\r
  63  * \r
  64  * @author Peter Troshin\r
  65  * @version 1.0 April 2011\r
  66  * \r
  67  */\r
  68 public class FastaReader implements Iterator<FastaSequence> {\r
  69 \r
  70         private final Scanner input;\r
  71         /**\r
  72          * Delimiter for the scanner\r
  73          */\r
  74         private final String DELIM=">";\r
  75         /**\r
  76          * Header data can contain non-ASCII symbols and read in UTF8\r
  77          * \r
  78          * @param inputFile\r
  79          *            the file containing the list of FASTA formatted sequences to\r
  80          *            read from\r
  81          * @throws FileNotFoundException\r
  82          *             if the input file is not found\r
  83          * @throws IllegalStateException\r
  84          *             if the close method was called on this instance\r
  85          * \r
  86          */\r
  87         public FastaReader(final String inputFile) throws FileNotFoundException {\r
  88                 input = new Scanner(new File(inputFile), "UTF8");\r
  89                 input.useDelimiter(DELIM);\r
  90                 Runtime.getRuntime().addShutdownHook(new Thread() {\r
  91 \r
  92                         @Override\r
  93                         public void run() {\r
  94                                 if (input != null) {\r
  95                                         input.close();\r
  96                                 }\r
  97                         }\r
  98                 });\r
  99         }\r
 100 \r
 101         /**\r
 102          * This class will not close the incoming stream! So the client should do\r
 103          * so.\r
 104          * \r
 105          * @param inputStream\r
 106          * @throws FileNotFoundException\r
 107          */\r
 108         public FastaReader(final InputStream inputStream)\r
 109                         throws FileNotFoundException {\r
 110                 input = new Scanner(inputStream);\r
 111                 input.useDelimiter(DELIM);\r
 112         }\r
 113         /**\r
 114          * {@inheritDoc}\r
 115          * \r
 116          * @throws IllegalStateException\r
 117          *             if the close method was called on this instance\r
 118          */\r
 119         @Override\r
 120         public boolean hasNext() {\r
 121                 return input.hasNext();\r
 122         }\r
 123 \r
 124         /**\r
 125          * Reads the next FastaSequence from the input\r
 126          * \r
 127          * @throws AssertionError\r
 128          *             if the header or the sequence is missing\r
 129          * @throws IllegalStateException\r
 130          *             if the close method was called on this instance\r
 131          *             @throws MismatchException - if there were no more FastaSequence's.\r
 132          */\r
 133         @Override\r
 134         public FastaSequence next() {\r
 135                 String fastaHeader=input.next();\r
 136                 while (fastaHeader.indexOf("\n")<0 && input.hasNext())\r
 137                 {\r
 138                         fastaHeader = fastaHeader.concat(">");\r
 139                         fastaHeader = fastaHeader.concat(input.next());\r
 140                 }\r
 141                 return FastaReader.toFastaSequence(fastaHeader);\r
 142         }\r
 143 \r
 144         /**\r
 145          * Not implemented\r
 146          */\r
 147         @Override\r
 148         public void remove() {\r
 149                 throw new UnsupportedOperationException();\r
 150         }\r
 151 \r
 152         /**\r
 153          * Call this method to close the connection to the input file if you want to\r
 154          * free up the resources. The connection will be closed on the JVM shutdown\r
 155          * if this method was not called explicitly. No further reading on this\r
 156          * instance of the FastaReader will be possible after calling this method.\r
 157          */\r
 158         public void close() {\r
 159                 input.close();\r
 160         }\r
 161 \r
 162         private static FastaSequence toFastaSequence(final String singleFastaEntry) {\r
 163 \r
 164                 assert !Util.isEmpty(singleFastaEntry) : "Empty String where FASTA sequence is expected!";\r
 165 \r
 166                 int nlineidx = singleFastaEntry.indexOf("\n");\r
 167                 if (nlineidx < 0) {\r
 168                         throw new AssertionError(\r
 169                                         "The FASTA sequence must contain the header information"\r
 170                                                         + " separated by the new line from the sequence. Given sequence does not appear to "\r
 171                                                         + "contain the header! Given data:\n "\r
 172                                                         + singleFastaEntry);\r
 173                 }\r
 174                 String header = singleFastaEntry.substring(0, nlineidx);\r
 175 \r
 176                 // Get rid of the new line chars (should cover common cases)\r
 177                 header = header.replaceAll("\r", "");\r
 178 \r
 179                 String sequence = singleFastaEntry.substring(nlineidx);\r
 180 \r
 181                 if (Util.isEmpty(sequence)) {\r
 182                         throw new AssertionError(\r
 183                                         "Empty sequences are not allowed! Please make sure the "\r
 184                                                         + " data is in the FASTA format! Given data:\n "\r
 185                                                         + singleFastaEntry);\r
 186                 }\r
 187                 return new FastaSequence(header, sequence);\r
 188         }\r
 189 }\r